i'm going to say it, Minecraft and Terraria, also been looking at this Cubeworld which is in Alpha apparently
I would also probably say Kamidori Alchemy Miester but i'm not sure if Eushully is indie or not, not to mention it's eroge and i run a patch onto of the English translation patch to block the H Scenes, it's still fun, going into maps, collecting resources, using alchemy to make stuff and sell it in your store or building up your heroine's armors, not to mention it's in a very big world that's been shaped by previous Eushully games, problem is that the Battle Goddess series is too old to translate (hard to get the games and how they were made) and Dungeon Miester apparently has a high amount of unavoidable heroine rape so it wont get translated either (even if it was i still wouldn't play it, even though it has Lilly but i don't want to see anything bad happen to her)
Type-Moon's games, they did start out as indie with Tsukihime so i'll talk about them, great story based games, Fate/, Mahou Tsukai no Yoru, even Melty Blood, i really want to put them out there so that we can get more support for the localization of Fate/Extra CCC since we can't call quits on Fate/Extra until we get out Far-Side of the Moon Heaven's Feel route
outside visual novels there's really only Recca-Tear (i think that's how it's spelled), how Extra Credits describe it is a game where "you play an Item Shop owner", i see it like Kamidori where while you have exploration to do you also have to manage your shop with the stuff you bring back, like in any large RPG you can't say you never wished that you wanted it to be real and make a living off exploring and selling your spoils